Yes... travelling across the seas should not be like what America mentioned in the beginning of his post.
The following is how I suggest it could be like:
Ships and boats:Yes, they come in all shapes and sizes,
(and materials). Basically, the era should decide the type of marine transport. Also proper navigation systems and life in sea can be portrayed (if possible)
1)If it's the old times, wooden ships, boats and rafts would be what you would usually spot in the saltwaters....2)If its the somewhat modern era, a couple of wooden ships and boats along with there metallic counterparts would be cool enough (imo, this would be ideal)If it's the modern era, those high tech battleships, carriers, cargos, motorboats, subs and motorafts is what one should expect in the seas. (I believe this is not what will happen as of now).Ownership:Now, who will own the boats?
Since I dunno whether we are gonna follow the kingdom system like in Naruto, I presume the
KAGE will be the supremo of the marine defense
(not exactly a navy) of her/his village.
Mostly I guess Shinobis of
Water or
wind nature will be in this force.
Lightning and
fire style ninjas can be useful in weaponry and maritime warfare.
Also, the Kage will have the right to choose whether she/he wants to have a
Marine Defense Force or not. And if yes, the Administrative structure of this organization can vary from village to village as per the kage and the village council.
Even clans can have their own boats and ships if they are the seafaring types.
Furthermore, talking about the civilian ownership of ships and boats, we can have NPCs in the form of fishermen, Businessmen, etc. who can have their own boats and cargos.
Control of marine territory:Each coastal village shall have a fixed area of seawater under their ownership. So the marine life, resources and water will be owned by a Kage in these areas. Entering without prior permission or trespassing can be punishable. The far fetched oceans can be
Free zone, where no Kage can have control.
Wars can happen to take control of these marine areas.
Pirates:Can't miss this one can we?

we can have NPCs as pirates,
(the non-shinobi ones). Whereas rogue ninjas can also form seafarering organization and can fall under the category of
Shinobi Pirates or Ninja kaizuke or anything you wanna call them other than rogue ninjas.
They could even be marine branches of Kata, Vongola and other rogue orgs.
Finally,
Miscellaneous stuffMysterious marine creatures: they could range from monsters to tiny useful legendary *(any other adjective)* organisms.
Battles: they can be caused by invasion, infiltration, unauthorized use of Kage's waters, strategic transport, attack and infiltration of troops during
Wars,etc.
Recreational: Annual sports like racing, shows to display marine strength of a village, etc.
To prevent stealing of ships and boats when it's owner or captain is not online is something of a problem since there would be some jerks who would like to go on joyrides in the sea...
I think, as a general purpose, when a player is offline, his property should be out of bound for online players.... just a thought..

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